RAB3D

RAB3D, member RAS oncogene family | D2-2, RAB16, RAD3D, GOV

Enables myosin V binding activity. Involved in bone resorption and positive regulation of regulated secretory pathway. Located in cytoplasmic microtubule and secretory vesicle. [provided by Alliance of Genome Resources, Jul 2025]

Member of: DE-4 Developmental clusters: GC7

Biological processes 25 terms

G protein activity (GO:0003925)G protein activity (GO:0003925)GTP binding (GO:0005525)GTP-dependent protein binding (GO:0030742)GTPase activity (GO:0003924)GTPase activity (GO:0003924)GTPase activity (GO:0003924)azurophil granule membrane (GO:0035577)bone resorption (GO:0045453)cytoplasmic microtubule (GO:0005881)endosome (GO:0005768)exocytosis (GO:0006887)extracellular exosome (GO:0070062)myosin V binding (GO:0031489)myosin V binding (GO:0031489)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane (GO:0005886)positive regulation of regulated secretory pathway (GO:1903307)protein binding (GO:0005515)regulation of exocytosis (GO:0017157)secretory granule (GO:0030141)secretory vesicle (GO:0099503)synaptic vesicle (GO:0008021)zymogen granule (GO:0042588)

Expression (TPM)

TFs regulating RAB3D 0 TFs

Transcription factors with Perturb-seq knockdown data for RAB3D. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = RAB3D upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

TF	Mean coef	Binding	Outlier	TF→Gene link

Rows:

Elements linked to RAB3D

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of RAB3D, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Element	Dist. to TSS	Link type	TFs
chr19:11,089,041–11,091,015	257.0 kb	Distal (>10kb) Multiome	964
chr19:11,137,551–11,138,233	208.4 kb	Distal (>10kb) Multiome	584
chr19:11,155,520–11,156,298	190.4 kb	Distal (>10kb) Multiome	754
chr19:11,196,759–11,198,184	148.6 kb	Distal (>10kb) Multiome	728
chr19:11,243,345–11,243,968	102.8 kb	Distal (>10kb) Multiome	448
chr19:11,262,060–11,262,653	83.8 kb	Distal (>10kb) Multiome	406
chr19:11,339,100–11,339,837	6.6 kb	Proximal (<10kb) Multiome	506
chr19:11,346,053–11,346,958	204 bp	At TSS Multiome	676
chr19:11,355,078–11,355,735	9.1 kb	Proximal (<10kb) Multiome	382
chr19:11,361,368–11,362,625	15.4 kb	Distal (>10kb) Multiome	256
chr19:11,374,474–11,375,717	28.7 kb	Distal (>10kb) Multiome	866
chr19:11,380,761–11,382,262	35.1 kb	Distal (>10kb) Multiome	798
chr19:11,382,830–11,384,509	38.1 kb	Distal (>10kb) Multiome	761
chr19:11,418,061–11,419,498	72.3 kb	Distal (>10kb) Multiome	421
chr19:11,420,614–11,422,979	75.9 kb	Distal (>10kb) Multiome	507
chr19:11,434,817–11,436,365	89.1 kb	Distal (>10kb) Multiome	927
chr19:11,479,217–11,480,146	133.4 kb	Distal (>10kb) Multiome	394
chr19:11,481,847–11,483,040	136.4 kb	Distal (>10kb) Multiome	938
chr19:11,504,741–11,506,612	159.1 kb	Distal (>10kb) Multiome	854
chr19:11,528,581–11,529,391	182.8 kb	Distal (>10kb) Multiome	866
chr19:11,535,847–11,536,353	189.9 kb	Distal (>10kb) Multiome	694
chr19:11,538,464–11,539,111	192.5 kb	Distal (>10kb) Multiome	235
chr19:11,539,738–11,540,434	193.8 kb	Distal (>10kb) Multiome	176
chr19:11,558,908–11,559,777	213.0 kb	Distal (>10kb) Multiome	686
chr19:11,597,206–11,598,107	251.2 kb	Distal (>10kb) Multiome	914
chr19:11,639,337–11,640,481	293.5 kb	Distal (>10kb) Multiome	660

Genome Browser

Genomic view of the RAB3D locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.